Après les attentats du 11 septembre 2001, la CIA se lance dans la guerre contre le terrorisme en pratiquant notamment des interrogatoires brutaux voire sadiques sur les détenus arrêtés et emprisonnés. Membre importante du Parti démocrate, la sénatrice Dianne Feinstein charge l'un de ses hommes, Daniel J. Jones, de mener une enquête sur leurs méthodes douteuses et immorales, dissimulées au peuple américain. Son investigation explosive révèle leur technique d'interrogatoire renforcée protégée et adoubée par le gouvernement américain, qui donna leur soutien et leur accord à la CIA pour qu'elle torture les suspects afin de leur soutirer des informations capitales. Après plusieurs années de recherches prouvant l'existence de ces pratiques cruelles passées sous silence, Jones rédige un rapport d'environ 500 pages, commandé par la United States Senate Select Committee on Intelligence, mais sa publication s'avère plus compliquée que prévu. En effet, la Maison-Blanche et la CIA mettent tout en œuvre pour étouffer les révélations de son enquête.
Après les attentats du 11 septembre 2001, une équipe composée d'agents de la CIA et des forces spéciales américaines, menées par le capitaine Mitch Nelson, est envoyée en Afghanistan. Ils collaborent avec le général afghan Abdul Rachid Dostom pour tenter de démanteler les talibans.
Cinq personnes sont bloquées dans un ascenseur de la tour nord du World Trade Center au matin du 11 septembre 2001, et tentent de s'échapper avant l'effondrement du bâtiment.
On the evening of September 11, 2012, the 11th anniversary of the September 11 attacks, a group of Islamic militants attack on the American diplomatic compound and a nearby CIA Annex in Benghazi, Libya. They kill four Americans, including a US Ambassador, J. Christopher Stevens. A security team of six members fight to defend Americans but only partially succeed.
In 2011, Anse Rainier (Gary Richardson), an American professor at Lahore University, is kidnapped soon after he leaves a movie theatre. A ransom video is sent to the US embassy, demanding the release of 690 detainees from a Muslim concentration camp in Kot Lakhpat and €700,000 for the children of Waziristan. Bobby Lincoln (Liev Schreiber), an American journalist and undercover CIA informant in Pakistan, arranges to interview a colleague of Rainer, Changez Khan (Riz Ahmed), who he suspects is involved in the kidnapping.
Nine-year-old Oskar Schell (Thomas Horn) is the son of German American Thomas Schell (Tom Hanks). Thomas would often send Oskar on missions to do something involving one of his riddles. The last riddle he ever gives Oskar is proof that New York City once possessed a Sixth Borough. In a flashback, Thomas and Oskar play a scavenger hunt to find objects throughout New York City. The game requires communication with other people and is not easy for the socially awkward Oskar who is told "If things were easy to find, they wouldn't be worth finding".
In 2003, Maya, a young U.S. Central Intelligence Agency officer, has spent her entire brief career, since graduating from college and being recruited for the agency, focused solely on gathering intelligence related to Osama bin Laden, leader of al-Qaeda, following the terrorist organization's attack on the United States in 2001. She is reassigned to the U.S. embassy in Pakistan to work with a fellow officer, Dan. During the first months of her assignment, Maya often accompanies Dan to a black site for his continuing interrogation of Ammar al-Baluchi, a detainee with suspected links to several of the hijackers in the September 11 attacks. Dan subjects the detainee to approved interrogation techniques, i.e., stress positions, hooding, subjection to deafening noise, sleep deprivation, waterboarding, and humiliation. After failing to get al-Baluchi to give up information on an attack in Saudi Arabia, he and Maya eventually trick Ammar into divulging that an old acquaintance, who is using the alias Abu Ahmed al-Kuwaiti, is working as a personal courier for bin Laden. Other detainees corroborate this, with some claiming Abu Ahmed delivers messages between bin Laden and a man known as Abu Faraj al-Libbi. In 2005, Abu Faraj is apprehended by the CIA and local police in Pakistan. Maya is allowed to interrogate him, but he continues to deny knowing a courier with such a name. Maya interprets this as an attempt by Faraj to conceal the importance of Abu Ahmed.
The film takes place in the same Queens police precinct in 1986 and 2002. In 2002, a young cop, Jonathan White, is a rookie officer under Captain Marion Mathers in a Queens neighborhood in New York City, where he grew up. To provide for his wife Kerry and ailing young daughter, he works hard to keep his life on track, but this life is threatened when a dark secret bubbles to the surface. An anonymous source reveals new information about two unsolved murders from 16 years ago. In 1986, Jonathan had killed two men in self-defense. His friends, Vinnie and Vicky, helped him dispose of the bodies and keep their involvement a secret from the authorities, and then Detective Stanford, who was the partner of Jonathan's deceased father, closes the cases, knowing he was involved.
Montine McLeod (Melissa Leo) is a flight attendant who gets stuck with Omar Hassan (Anthony Keyvan) after their flight gets grounded in Longview, Texas, the morning of 11 September 2001. Omar is an unaccompanied minor; in the chaos that ensues, Montine becomes his temporary guardian. Montine later discovers that Omar's father works in the World Trade Center. She decides to drive the boy home after he informs her his father is at home waiting for him in New York. On the journey, they begin to bond and learn more about each other. Montine makes a stop on the way to New York as she receives a call that her mother is dying. Upon arriving at her mother's house, she finds her mother already dead. After dealing with her mother's death, she continues on the road to take Omar home. When they get there, they learn Omar's father has not been home in the two days since the destruction of the Twin Towers. Later that night, Montine receives a call from her employer and is forced to bring Omar with her. At the ensuing meeting, Montine is terminated; Omar is taken from her and given to his school head master for the night before leaving for a new school the following day (the reason he was on the original flight). The day Omar is set to leave for Los Angeles, he locks himself in the bathroom and refuses to come out. Montine is asked to come; she coaxes Omar out of the bathroom and she walks him to his flight to Los Angeles.
Ranveer Singh is shocked when his younger brother living in the US is killed in a post-9/11 hate crime. He travels to Los Angeles to bring his brother's murderers to justice. There he meets former LAPD officer Fateh Singh and Pakistani American Rizwan Hyder who help him uncover the truth of what really happened.